Welcome to the Dr. Peifeng Ruan Lab!

I am an Assistant Professor at the Quantitative Biomedical Research Center at UT Southwestern Medical Center (UTSW). Before arriving at UTSW, I completed my postdoctoral training in the Department of Biostatistics at Yale University. I received my Ph.D. degree in Biostatistics from The George Washington University and my Ph.D. degree in Computer Science at Fudan University.

Our lab's research interests focus on developing statistical methods and computational algorithms for multi-omics data with applications in complex human diseases, such as heart disease and cancer.

Research Interests

Multi-omics integration

Statistical analysis of network data

High dimensional data analysis

Latest Publications

A complete publication list can be found here.

MORE PUBLICATIONS
Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis

Yue Ren, Peifeng Ruan, Mark Segal, Mirela Dobre, Jeffrey R Schelling, Upasana Banerjee, Tariq Shafi, Peter Ganz, Ruth F Dubin, CRIC Study Investigators (2023)
PloS one 18 (12), e0293945

publisher's website

Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression

Peifeng Ruan, Jamie L Todd, Hongyu Zhao, Yi Liu, Richard Vinisko, Julia F Soellner, Ramona Schmid, Robert J Kaner, Tracy R Luckhardt, Megan L Neely, Imre Noth, Mary Porteous, Rishi Raj, Zeenat Safdar, Mary E Strek, Christian Hesslinger, Scott M Palmer, Thomas B Leonard, Margaret L Salisbury (2023).
Respiratory Research

publisher's website

DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes

P Ruan, S Wang (2021).
Briefings in Bioinformatics 22 (4), bbaa241

publisher's website

Research Interests

  • Multi-omics integration

    Publications

    Ruan, P., Todd, J.L., Zhao, H., Liu, Y., Vinisko, R., Soellner, J.F., Schmid, R., Kaner, R.J., Luckhardt, T.R., Neely, M.L. and Noth, I., 2023. Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression. Respiratory Research, 24(1), p.141.
    Ruan, P., Wang, Y., Shen, R. and Wang, S., 2019. Using association signal annotations to boost similarity network fusion. Bioinformatics, 35(19), pp.3718-3726.
    Ren, Y., Ruan, P., Segal, M., Dobre, M., Schelling, J.R., Banerjee, U., Shafi, T., Ganz, P., Dubin, R.F. and CRIC Study Investigators, 2023. Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis. PloS one, 18(12), p.e0293945.

  • Statistical analysis of network data

    Publications

    Ruan, P. and Wang, S., 2021. DiSNEP: a disease-specific gene network enhancement to improve prioritizing candidate disease genes. Briefings in Bioinformatics, 22(4), p.bbaa241.
    Ruan, P., Shen, J., Santella, R.M., Zhou, S. and Wang, S., 2016. NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals. Nucleic acids research, 44(16), pp.e134-e134.
    Wang, Y., Qian, M., Ruan, P., Teschendorff, A.E. and Wang, S., 2019. Detection of epigenetic field defects using a weighted epigenetic distance-based method. Nucleic acids research, 47(1), pp.e6-e6.

  • High dimensional data analysis

    Publications

    Ruan, P., Wang, S. and Liang, H., 2020. mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs. Bioinformatics, 36(19), pp.4902-4909.
    Huang, H., Shangguan, J., Ruan, P. and Liang, H., 2019. Bi-level feature selection in high dimensional AFT models with applications to a genomic study. Statistical applications in genetics and molecular biology, 18(5).

Software

  • DiSNEP

    Link

    - R package for an improved analytical tool for prioritizing genes associated with diseases using gene network information.
    - Reference: Ruan, P. and Wang S. DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes. Accepted by Briefings in Bioinformatics.

  • mirPLS

    Link

    - R package for a partial linear structure identifier algorithm identifying non-linearly outcome-associated miRNAs for cancer subtyping.
    - Reference: Ruan, P., Wang, S. and Liang, H. mirPLS: A Partial Linear Structure Identifier Method for Cancer Subtyping Using MicroRNAs. Bioinformatics, btaa606.

  • abSNF

    Link

    - R package for an algorithm using association signal annotation to boost similarity network fusion for diseases subtyping.
    - Reference: Ruan, P., Wang, Y., Shen, R., and Wang, S. (2019). Using Association Signal Annotations to Boost Similarity Network Fusion.Bioinformatics, 35(19): 3718-3726.

  • NEpiC

    Link

    - R package for a biological network assisted greedy algorithm for identifying epigenetic biomarkers.
    - Reference: Ruan, P., Shen, J., Santella, R. M., Zhou, S., and Wang, S. (2016) NEpiC: a Network-Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals. Nucleic Acids Research, 44(16), e134-e134.

Publications

Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis

Yue Ren, Peifeng Ruan, Mark Segal, Mirela Dobre, Jeffrey R Schelling, Upasana Banerjee, Tariq Shafi, Peter Ganz, Ruth F Dubin, CRIC Study Investigators
Dec. 2023PloS one 18 (12), e0293945

Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression

Peifeng Ruan, Jamie L Todd, Hongyu Zhao, Yi Liu, Richard Vinisko, Julia F Soellner, Ramona Schmid, Robert J Kaner, Tracy R Luckhardt, Megan L Neely, Imre Noth, Mary Porteous, Rishi Raj, Zeenat Safdar, Mary E Strek, Christian Hesslinger, Scott M Palmer, Thomas B Leonard, Margaret L Salisbury
Dec. 2023Respiratory Research 24 (1), 1-12

DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes

P Ruan, S Wang
July 2021Briefings in Bioinformatics 22 (4), bbaa241

mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs

P Ruan, S Wang, H Liang
Oct. 2020Bioinformatics 36 (19), 4902-4909

Advanced Statistical Models in Cancer Research with Omics Data

P Ruan
2020The George Washington University

Detection of Epigenetic Field Defects Using a Weighted Epigenetic Distance-Based Method

Y Wang, M Qian, P Ruan, AE Teschendorff, S Wang
2020Stem Cell Transcriptional Networks, 109-131

Using association signal annotations to boost similarity network fusion

P Ruan, Y Wang, R Shen, S Wang
Oct. 2019Bioinformatics 35 (19), 3718-3726

Bi-level feature selection in high dimensional AFT models with applications to a genomic study

H Huang, J Shangguan, P Ruan, H Liang
Oct. 2019Statistical applications in genetics and molecular biology 18 (5)

Detection of epigenetic field defects using a weighted epigenetic distance-based method

Y Wang, M Qian, P Ruan, AE Teschendorff, S Wang
Jan. 2019Nucleic acids research 47 (1), e6-e6

NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals

P Ruan, J Shen, RM Santella, S Zhou, S Wang
Sept. 2016BioRxiv, 382549

Members

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Bo Yao
Scientific Programmer III
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Peiran Quan
Database Scientist
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Ismael Villanueva-Miranda
Data Scientist II

About PI

Peifeng Ruan

Assistant Professor, Quantitative Biomedical Research Center, UT Southwestern Medical Center
  Peifeng.Ruan@​UTSouthwestern​.edu
  5323 Harry Hines Blvd. Dallas, TX 75390
Download CV

Biography

I am an Assistant Professor at the Quantitative Biomedical Research Center at UT Southwestern Medical Center (UTSW). Before arriving at UTSW, I completed my postdoctoral training in the Department of Biostatistics at Yale University. I received my Ph.D. degree in Biostatistics from The George Washington University and my Ph.D. degree in Computer Science at Fudan University.

Our lab's research interests focus on developing statistical methods and computational algorithms for multi-omics data with applications in complex human diseases, such as heart disease and cancer.

Positions and Scientific Appointments

  • present 2022
    Assistant Professor
    UT Southwestern Medical Center, Dallas, TX
  • 2022 2020
    Postdoctoral Associate
    Joint program with Boehringer Ingelheim
    Yale University, New Haven, CT
  • 2015 2014
    Visiting Scholar
    Columbia University Medical Center, New York, NY

Education

  • 2020 2016
    Ph.D. in Biostatistics
    The George Washington University, Washington, DC
  • 2015 2010
    Ph.D. in Computer Science
    Fudan University, Shanghai, China
  • 2012 2011
    M.A. in Statistics
    Columbia University, New York, NY
  • 2010 2006
    B.S. in Applied Mathematics
    Fudan University, Shanghai, China